Seems like analogWrite() works because 9,10 and 11 are PWM pins? SHould I be looking into digitalWrite at all?
Do you want the LED's color segments to have their brightness correlated to the values you are passing from your processing sketch? If yes, then analogWrite() and PWM are your only options.
If you just want to turn on the color segments based on the value then you can use digitalWrite() and if statements.
As CrossRoads points out, you can't make multiple calls to Serial.read(). Each time you do, the buffer gets flushed.